Supercoiling is Necessary for Packaging of Bacterial DNA

An average bacterial cell is about one millionth of a meter long. The length of the single DNA molecule needed to carry the 4,000 or so genes of a bacterial cell is about one millimeter! Thus, a stretched out bacterial chromosome is a thousand times longer than a bacterial cell. The double helical DNA inside a cell must be supercoiled to make it more compact. The DNA, which is already a double helix, is twisted again, as shown in Figure 4.15. The original double helix has a right-handed twist but the supercoils twist in the opposite sense; that is, they are left-handed or "negative" supercoils. There is roughly one supercoil every 200 nucleotides in typical bacterial DNA. Negative (rather than positive) supercoiling helps promote the unwinding and strand separation necessary during replication and transcription. [Eukaryotic DNA is also negatively supercoiled, however the mechanism is rather different and involves coiling it around histone proteins as discussed below.]

Negative supercoils are introduced into the bacterial chromosome by DNA gyrase. In the absence of topoisomerase I and topoisomerase IV, the DNA becomes hyper-negatively supercoiled. The steady-state level of supercoiling in Escherichia coli is maintained by a balance between topoisomerase IV, acting in concert with topoiso-merase I, to remove excess negative supercoils and thus acting in opposition to DNA gyrase. A typical bacterial chromosome contains approximately 50 giant loops of super-coiled DNA arranged around a protein scaffold. In Figure 4.16, the single line represents a double helix of DNA and the helixes are the supercoils.

bent DNA Double helical DNA that is bent due to several runs of As negative supercoiling Supercoiling with a left handed or counterclockwise twist supercoiling Higher level coiling of DNA that is already a double helix

Topoisomerases and DNA Gyrase 89

FIGURE 4.15 Supercoiling of DNA

Bacterial DNA is negatively supercoiled in addition to the twisting imposed by the double helix.

Circular DNA

Negatively supercoiled DNA

FIGURE 4.16 Supercoiling of the Bacterial Chromosome

Supercoiling of bacterial DNA results in giant loops of supercoiled DNA extending from a central scaffold.

FIGURE 4.16 Supercoiling of the Bacterial Chromosome

Supercoiling of bacterial DNA results in giant loops of supercoiled DNA extending from a central scaffold.

The bacterial chromosome consists of about 50 giant supercoiled loops of DNA.

Bacterial chromosomes and plasmids are double stranded circular DNA molecules and are often referred to as covalently closed circular DNA, or cccDNA. If one strand of a double stranded circle is nicked, the supercoiling can unravel. Such a molecule is known as an open circle.

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